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-   -   Best tool to find gene variants in metagenome data (http://seqanswers.com/forums/showthread.php?t=77708)

vsnishtala 08-23-2017 03:52 AM

Best tool to find gene variants in metagenome data
 
hey ,

I was wondering did some body know any tools to find gene variants in metagenome data? I know about the freebayes and GATK, but which one is ideal to use on metgenome data and are there any other tools or pipelines to follow.

Brian Bushnell 08-23-2017 09:52 AM

I don't know what's best for metagenome variant-calling, but a couple of additional options are Samtools mpilup + bcftools, and BBMap's CallVariants. I wrote a suggested variant-calling pipeline in the BBMap page, at bbmap/pipelines/variantPipeline.sh, which gives an example of how to preprocess the data and call variants.

vsnishtala 08-24-2017 02:34 PM

Quote:

Originally Posted by Brian Bushnell (Post 210354)
I don't know what's best for metagenome variant-calling, but a couple of additional options are Samtools mpilup + bcftools, and BBMap's CallVariants. I wrote a suggested variant-calling pipeline in the BBMap page, at bbmap/pipelines/variantPipeline.sh, which gives an example of how to preprocess the data and call variants.

Thank you Brain Bushnell i will look into it !


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